dev-lang/R: Version BUmp, #486064

(Portage version: 2.2.7/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!)

3 files changed, 218 insertions, 7 deletions

diff --git a/dev-lang/R/ChangeLog b/dev-lang/R/ChangeLog
index a9af427d139a..cfcf4dbf4cdc 100644
--- a/dev-lang/R/ChangeLog
+++ b/dev-lang/R/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for dev-lang/R
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/dev-lang/R/ChangeLog,v 1.218 2013/09/24 16:13:24 bicatali Exp $
+# $Header: /var/cvsroot/gentoo-x86/dev-lang/R/ChangeLog,v 1.219 2013/09/26 13:55:24 jlec Exp $
+
+*R-3.0.2 (26 Sep 2013)
+
+  26 Sep 2013; Justin Lecher <jlec@gentoo.org> +R-3.0.2.ebuild, metadata.xml:
+  Version BUmp, #486064
 
 *R-3.0.1-r1 (24 Sep 2013)
 
diff --git a/dev-lang/R/R-3.0.2.ebuild b/dev-lang/R/R-3.0.2.ebuild
new file mode 100644
index 000000000000..b418fbd5e24d
--- /dev/null
+++ b/dev-lang/R/R-3.0.2.ebuild
@@ -0,0 +1,206 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/dev-lang/R/R-3.0.2.ebuild,v 1.1 2013/09/26 13:55:24 jlec Exp $
+
+EAPI=5
+
+inherit bash-completion-r1 autotools eutils flag-o-matic fortran-2 multilib versionator toolchain-funcs
+
+BCP=${PN}-20130129.bash_completion
+DESCRIPTION="Language and environment for statistical computing and graphics"
+HOMEPAGE="http://www.r-project.org/"
+SRC_URI="
+	mirror://cran/src/base/R-3/${P}.tar.gz
+	bash-completion? ( http://dev.gentoo.org/~bicatali/distfiles/${BCP}.bz2 )"
+
+LICENSE="|| ( GPL-2 GPL-3 ) LGPL-2.1"
+SLOT="0"
+KEYWORDS="~alpha ~amd64 ~hppa ~ia64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-fbsd ~x86-linux ~x64-macos"
+IUSE="bash-completion cairo doc icu java jpeg lapack minimal nls openmp perl png prefix profile readline static-libs tiff tk X"
+REQUIRED_USE="png? ( || ( cairo X ) ) jpeg? ( || ( cairo X ) ) tiff? ( || ( cairo X ) )"
+
+CDEPEND="
+	app-arch/bzip2
+	app-text/ghostscript-gpl
+	dev-libs/libpcre
+	app-misc/realpath
+	virtual/blas
+	cairo? ( x11-libs/cairo[X] x11-libs/pango )
+	icu? ( dev-libs/icu )
+	jpeg? ( virtual/jpeg:0 )
+	lapack? ( virtual/lapack )
+	perl? ( dev-lang/perl )
+	png? ( media-libs/libpng )
+	readline? ( sys-libs/readline )
+	tk? ( dev-lang/tk )
+	X? ( x11-libs/libXmu x11-misc/xdg-utils )"
+
+DEPEND="${CDEPEND}
+	virtual/pkgconfig
+	doc? (
+			virtual/latex-base
+			dev-texlive/texlive-fontsrecommended
+		 )"
+
+RDEPEND="${CDEPEND}
+	( || ( <sys-libs/zlib-1.2.5.1-r1 >=sys-libs/zlib-1.2.5.1-r2[minizip] ) )
+	app-arch/xz-utils
+	java? ( >=virtual/jre-1.5 )"
+
+RESTRICT="minimal? ( test )"
+
+R_DIR="${EROOT%/}/usr/$(get_libdir)/${PN}"
+
+pkg_setup() {
+	if use openmp; then
+		FORTRAN_NEED_OPENMP=1
+		tc-has-openmp || die "Please enable openmp support in your compiler"
+	fi
+	fortran-2_pkg_setup
+	filter-ldflags -Wl,-Bdirect -Bdirect
+	# avoid using existing R installation
+	unset R_HOME
+	# Temporary fix for bug #419761
+	if [[ ($(tc-getCC) == *gcc) && ($(gcc-version) == 4.7) ]]; then
+		append-flags -fno-ipa-cp-clone
+	fi
+}
+
+src_prepare() {
+	# gentoo bug #322965 (not applied upstream)
+	# https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=14505
+	epatch "${FILESDIR}"/${PN}-2.11.1-parallel.patch
+
+	# respect ldflags (not applied upstream)
+	# https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=14506
+	epatch "${FILESDIR}"/${PN}-2.12.1-ldflags.patch
+
+	# gentoo bug #383431
+	# https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=14951
+	epatch "${FILESDIR}"/${PN}-2.13.1-zlib_header_fix.patch
+
+	# https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=14953
+	epatch "${FILESDIR}"/${PN}-3.0.0-rmath-shared.patch
+
+	# fix packages.html for doc (gentoo bug #205103)
+	sed -i \
+		-e "s:../../../library:../../../../$(get_libdir)/R/library:g" \
+		src/library/tools/R/Rd.R || die
+
+	# fix Rscript path when installed (gentoo bug #221061)
+	sed -i \
+		-e "s:-DR_HOME='\"\$(rhome)\"':-DR_HOME='\"${R_DIR}\"':" \
+		src/unix/Makefile.in || die "sed unix Makefile failed"
+
+	# fix HTML links to manual (gentoo bug #273957)
+	sed -i \
+		-e 's:\.\./manual/:manual/:g' \
+		$(grep -Flr ../manual/ doc) || die "sed for HTML links failed"
+
+	use lapack && \
+		export LAPACK_LIBS="$($(tc-getPKG_CONFIG) --libs lapack)"
+
+	if use X; then
+		export R_BROWSER="$(type -p xdg-open)"
+		export R_PDFVIEWER="$(type -p xdg-open)"
+	fi
+	use perl && \
+		export PERL5LIB="${S}/share/perl:${PERL5LIB:+:}${PERL5LIB}"
+
+	# don't search /usr/local
+	sed -i -e '/FLAGS=.*\/local\//c\: # removed by ebuild' configure.ac || die
+	# Fix for Darwin (OS X)
+	if use prefix; then
+		if [[ ${CHOST} == *-darwin* ]] ; then
+			sed -i \
+				-e 's:-install_name libR.dylib:-install_name ${libdir}/R/lib/libR.dylib:' \
+				-e 's:-install_name libRlapack.dylib:-install_name ${libdir}/R/lib/libRlapack.dylib:' \
+				-e 's:-install_name libRblas.dylib:-install_name ${libdir}/R/lib/libRblas.dylib:' \
+				-e "/SHLIB_EXT/s/\.so/.dylib/" \
+				configure.ac || die
+			# sort of "undo" 2.14.1-rmath-shared.patch
+			sed -i \
+				-e "s:-Wl,-soname=libRmath.so:-install_name ${EROOT%/}/usr/$(get_libdir)/libRmath.dylib:" \
+				src/nmath/standalone/Makefile.in || die
+		else
+			append-ldflags -Wl,-rpath="${EROOT%/}/usr/$(get_libdir)/R/lib"
+		fi
+	fi
+	AT_M4DIR=m4 eaclocal
+	eautoconf
+}
+
+src_configure() {
+	econf \
+		--enable-byte-compiled-packages \
+		--enable-R-shlib \
+		--disable-R-framework \
+		--with-system-zlib \
+		--with-system-bzlib \
+		--with-system-pcre \
+		--with-system-xz \
+		--with-blas="$($(tc-getPKG_CONFIG) --libs blas)" \
+		--docdir="${EPREFIX}/usr/share/doc/${PF}" \
+		rdocdir="${EPREFIX}/usr/share/doc/${PF}" \
+		$(use_enable nls) \
+		$(use_enable openmp) \
+		$(use_enable profile R-profiling) \
+		$(use_enable profile memory-profiling) \
+		$(use_enable static-libs static) \
+		$(use_enable static-libs R-static-lib) \
+		$(use_with cairo) \
+		$(use_with icu ICU) \
+		$(use_with jpeg jpeglib) \
+		$(use_with lapack) \
+		$(use_with !minimal recommended-packages) \
+		$(use_with png libpng) \
+		$(use_with readline) \
+		$(use_with tiff libtiff) \
+		$(use_with tk tcltk) \
+		$(use_with X x)
+}
+
+src_compile() {
+	export VARTEXFONTS="${T}/fonts"
+	emake AR="$(tc-getAR)"
+	emake -C src/nmath/standalone shared $(use static-libs && echo static) AR="$(tc-getAR)"
+	use doc && emake info pdf
+}
+
+src_install() {
+	default
+	emake -j1 -C src/nmath/standalone DESTDIR="${D}" install
+
+	if use doc; then
+		emake DESTDIR="${D}" install-info install-pdf
+		dosym ../manual /usr/share/doc/${PF}/html/manual
+	fi
+
+	cat > 99R <<-EOF
+		LDPATH=${R_DIR}/lib
+		R_HOME=${R_DIR}
+	EOF
+	doenvd 99R
+	use bash-completion && newbashcomp "${WORKDIR}"/${BCP} ${PN}
+	# The buildsystem has a different understanding of install_names than what
+	# we require.  Since it builds modules like shared objects (wrong), many
+	# objects (all modules) get an incorrect install_name.  Fixing the build
+	# system here is not really trivial.
+	if [[ ${CHOST} == *-darwin* ]] ; then
+		local mod
+		pushd "${ED}"/usr/lib/R > /dev/null
+		for mod in $(find . -name "*.dylib") ; do
+			mod=${mod#./}
+			install_name_tool -id "${EPREFIX}/usr/lib/R/${mod}" \
+				"${mod}"
+		done
+		popd > /dev/null
+	fi
+}
+
+pkg_postinst() {
+	if use java; then
+		einfo "Re-initializing java paths for ${P}"
+		R CMD javareconf
+	fi
+}
diff --git a/dev-lang/R/metadata.xml b/dev-lang/R/metadata.xml
index 5d205a8da7fb..1deadcbddd09 100644
--- a/dev-lang/R/metadata.xml
+++ b/dev-lang/R/metadata.xml
@@ -1,12 +1,12 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-<herd>sci-mathematics</herd>
-<maintainer>
-  <email>calchan@gentoo.org</email>
-  <name>Denis Dupeyron</name>
-</maintainer>
-<longdescription lang="en">
+  <herd>sci-mathematics</herd>
+  <maintainer>
+    <email>calchan@gentoo.org</email>
+    <name>Denis Dupeyron</name>
+  </maintainer>
+  <longdescription lang="en">
   R is GNU S, a system for statistical computation and graphics. It
   consists of a language plus a run-time environment with graphics, a
   debugger, access to certain system functions, and the ability to run